Chi8: a GPU program for detecting significant interacting SNPs with the Chi-square 8-df test

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Al-jouie, Abdulrhman; Esfandiari, Mohammadreza; Ramakrishnan, Srividya; Roshan, Usman;
(2015)
  • Publisher: Springer Nature
  • Journal: BMC Research Notes,volume 8 (issn: 1756-0500, eissn: 1756-0500)
  • Related identifiers: pmc: PMC4568583, doi: 10.1186/s13104-015-1392-5
  • Subject: Biochemistry, Genetics and Molecular Biology(all) | Epistasis | Chi-square 8 degrees of freedom | Graphics Processing Unit | Medicine(all) | Technical Note | Genome wide association studies | Interacting SNPs

Background Determining interacting SNPs in genome-wide association studies is computationally expensive yet of considerable interest in genomics. Findings We present a program Chi8 that calculates the Chi-square 8 degree of freedom test between all pairs of SNPs in a br... View more
  • References (24)
    24 references, page 1 of 3

    1. Marchini J, Donnelly P, Cardon LR. Genome‑ wide strategies for detecting multiple loci that influence complex diseases. Nat Genet. 2005;37(4):413-7.

    2. Wang Y, Liu G, Feng M, Wong L. An empirical comparison of several recent epistatic interaction detection methods. Bioinformatics. 2011;27(21):2936-43. doi:10.1093/bioinformatics/btr512.

    3. Zhang X, Huang S, Zou F, Wang W. Team: eficient two ‑locus epistasis tests in human genome‑ wide association study. Bioinformatics. 2010;26(12):217-27. doi:10.1093/bioinformatics/btq186.

    4. Ritchie MD, Hahn LW, Roodi N, Bailey LR, Dupont WD, Parl FF, Moore JH. Multifactor‑ dimensionality reduction reveals high‑ order interactions among estrogen‑metabolism genes in sporadic breast cancer. Am J Hum Genet. 2001;69:138-47. doi:10.1086/321276.

    5. Prabhu S, Pe'er I. Ultrafast genome‑ wide scan for SNP-SNP interactions in common complex disease. Genome Res. 2012;22(11):2230-40.

    6. Wu J, Devlin B, Ringquist S, Trucco M, Roeder K. Screen and clean: a tool for identifying interactions in genome‑ wide association studies. Genet Epidemiol. 2010;34(3):275-85. doi:10.1002/gepi.20459.

    7. Yang C, He Z, Wan X, Yang Q, Xue H, Yu W. Snpharvester: a filtering‑based approach for detecting epistatic interactions in genome‑ wide association studies. Bioinformatics. 2009;25(4):504-11. doi:10.1093/bioinformatics/ btn652.

    8. Hu X, Liu Q, Zhang Z, Li Z, Wang S, He L, Shi Y. SHEsisEpi, a GPUenhanced genome‑ wide SNP-SNP interaction scanning algorithm, eficiently reveals the risk genetic epistasis in bipolar disorder. Cell Res. 2010;20(7):854-7.

    9. Kam‑ Thong T, Czamara D, Tsuda K, Borgwardt K, Lewis CM, ErhardtLehmann A, Hemmer B, Rieckmann P, Daake M, Weber F. Epiblaster‑fast exhaustive two‑locus epistasis detection strategy using graphical processing units. Eur J Hum Genet. 2010;19(4):465-71.

    10. Yung LS, Yang C, Wan X, Yu W. GBOOST: a GPU‑based tool for detecting gene-gene interactions in genome‑ wide case control studies. Bioinformatics. 2011;27(9):1309-10.

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